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Table 1 Primers and probes used in qPCR assays

From: Quantitative PCR of ear discharge from Indigenous Australian children with acute otitis media with perforation supports a role for Alloiococcus otitidis as a secondary pathogen

Assay

Gene

Primer and Probe sequences

Position

Amplicon size (bp)

Reference

Ao

16S rRNA

Forward primer 5'- CTACGCATTTCACCGCTACAC -3'

437-457

265

[33]

Reverse primer 5'- GGGGAAGAACACGGATAGGA -3'

702-483

TBL

16S rRNA

Forward primer 5'- TCCTACGGGAGGCAGCAGT -3'

331-349

466

[6, 36]

Reverse primer 5'- GGACTACCAGGGTATCTAATCCTGTT -3'

797-772

Hi

hpd

Forward primer 5’- GGTTAAATATGCCGATGGTGTTG -3’

822-844

151

[37, 38]

Reverse primer 5’- TGCATCTTTACGCACGGTGTA -3’

972-953

Probe 5’Hex- TTGTGTACACTCCGT “T” GGTAAAAGAACTTGCAC -SpC6 -3’*

928-896

Spn

lytA

Forward primer 5'- TCTTACGCAATCTAGCAGATGAAGC -3'

306-326

101

[6]

Reverse primer 5'- GTTGTTTGGTTGGTTATTCGTGC -3'

406-386

Probe 5'- [6-FAM]-TTTGCCGAAAACGCTTGATACAGGG -[TAMRA] -3'

354-330

Mc

copB

Forward primer 5'- GTGAGTGCCGCTTTTACAACC -3'

50-70

72

[6]

Reverse primer 5'- TGTATCGCCTGCCAAGACAA -3'

121-102

  1. Ao = A. otitidis. TBL = Total bacterial load. Spn = S. pneumoniae. Hi = H. influenzae. Mc = M. catarrhalis. 16S rRNA gene position numbers are based on E. coli numbering. * Inverted commas in the primer sequence of the hpd probe indicate the position of the Black Hole Quencher.